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Author SHA1 Message Date
Nicola Soranzo 5dcafe752b Update Celery and Kombu links 2022-05-06 13:29:14 +01:00
Nicola Soranzo 9cd73e20c9 Fix typo in f-string 2022-05-06 13:29:13 +01:00
Nicola Soranzo 6ab35f4817 Fix error message from `ExpressionValidator` 
when the expression could not be evaluated. Previously the message
would be:
```
Validator '<code object <module> at 0x7fcfdf6737c0, file "<string>", line 1>' could not be evaluated on '%s'
```

Also, move doc tests to unit tests.
 2022-05-06 13:29:13 +01:00
Nicola Soranzo a586ecd784 Use `listify() to split ensure_channels`; add type annotation 2022-05-06 12:37:48 +01:00
Marius van den Beek 131e1d464d Merge pull request #13641 from simonbray/wf-step-index 
Expose input step order and rework calculation of node position in the workflow editor
 2022-05-06 12:37:52 +02:00
Marius van den Beek 0ca4110d40 Merge pull request #13872 from natefoo/quieter-galaxy-tool-test 
Don't reprint a traceback that has already been printed at the end of galaxy-tool-test
 2022-05-06 12:35:01 +02:00
Marius van den Beek ed451ccc55 Merge pull request #13874 from dannon/add-client-build-to-app 
Add client build timestamp to application config.
 2022-05-06 12:33:44 +02:00
Marius van den Beek b61f807c74 Merge pull request #13875 from jmchilton/invocations_view_enum 
Use an Enum for invocations view.
 2022-05-06 12:32:39 +02:00
Dannon Baker 0a3ca4f8b5 Decorate userHistories jest test for retry for now 2022-05-05 19:50:57 -04:00
Björn Grüning d1fc41c990 Merge pull request #13867 from jmchilton/workflow_index_fixes 
Workflow Index Fixes and Improvements
 2022-05-06 00:06:36 +02:00
John Chilton cee1ad0ba8 Merge pull request #13870 from jmchilton/pages_api_paginate 
Pages Index API Improvements
 2022-05-05 17:11:33 -04:00
John Chilton d2feecd443 Bugfix - allow filtering on multiple workflow tags at once. 2022-05-05 15:22:32 -04:00
John Chilton d2601426a4 index_filter_util to re-use filters from workflows in other index models. 2022-05-05 15:22:32 -04:00
John Chilton 836ae62495 Move workflows index query operations into the manager layer. 2022-05-05 15:22:32 -04:00
John Chilton caa5c56a0a Allow filtering workflows on sharing tags. 
Implement is:published and is:shared_with_me in the query 'search' parameter.
 2022-05-05 15:22:32 -04:00
John Chilton d2e555d0a7 Docs for workflow index filter tags. 2022-05-05 15:22:32 -04:00
John Chilton 277c57008b Use an Enum for invocations view. 2022-05-05 14:40:20 -04:00
John Chilton c933732b1d Fix stray non-breaking typo in workflows.py. 2022-05-05 14:31:57 -04:00
Marius van den Beek 1d7ef8cd35 Merge pull request #13862 from jmchilton/invocations_service 
Refactor toward invocations service layer.
 2022-05-05 20:09:16 +02:00
John Chilton 4a53effe22 Implement sorting, limiting, and offset in pages index. 2022-05-05 14:02:20 -04:00
John Chilton f7c259d8cb Implement show_published and show_shared in pages index to match workflows. 2022-05-05 14:02:20 -04:00
John Chilton 362ed5ccc8 Allow filtering pages query by user_id. 2022-05-05 14:02:20 -04:00
John Chilton fee7f154ad Refactor pages index plumbing for expansion. 2022-05-05 14:02:20 -04:00
John Chilton bf89f69cc9 Readability improvement in test_pages.py. 2022-05-05 14:02:20 -04:00
Dannon Baker a0fcec1d47 Attach to basic onload instead of GalaxyApp; no need to hang it off the object 2022-05-05 13:51:41 -04:00
Dannon Baker 43f5f12190 Plug clientBuildInfo into Galaxy app 
Documentation; fix eslint no-undef
 2022-05-05 13:49:00 -04:00
Nate Coraor 184416a811 Don't reprint a traceback that has already been printed at the end of galaxy-tool-test 2022-05-05 11:34:02 -04:00
Marius van den Beek 0e96433199 Merge pull request #13833 from jdavcs/dev_dataset_declarative 
Map Dataset declaratively
 2022-05-05 17:06:33 +02:00
Marius van den Beek ddbd8bd8c5 Merge pull request #13811 from gmauro/IT_updates 
IT updates from EU
 2022-05-05 17:02:55 +02:00
Simon Bray 3f42b7a0a9 Merge branch 'wf-step-index' of github.com:simonbray/galaxy into wf-step-index 2022-05-05 16:10:29 +02:00
Simon Bray 77012ce7f5 Merge remote-tracking branch 'upstream/dev' into wf-step-index 2022-05-05 16:01:36 +02:00
John Chilton 0c10235510 Refactor toward invocations service layer. 2022-05-05 08:19:57 -04:00
John Chilton d12f7c8596 Merge pull request #13861 from jmchilton/model_store_typing 
Improved typing of Galaxy model store related stuff.
 2022-05-05 07:30:54 -04:00
Marius van den Beek e54147b69d Merge pull request #13863 from mr-c/patch-1 
galaxy-tool-util: better link in the README
 2022-05-05 10:30:17 +02:00
Marius van den Beek 7779bdfbf3 Merge pull request #13857 from jmchilton/bookmark_fix 
Fix workflow bookmarking API.
 2022-05-05 10:27:57 +02:00
Björn Grüning ee617663c6 Merge pull request #13864 from nsoranzo/CI_updates 
Various CI fixes and enhancements
 2022-05-05 10:19:33 +02:00
Björn Grüning 23177162eb Merge pull request #13855 from jmchilton/more_robust_workflow_tests 
More robust workflow grid selenium tests.
 2022-05-05 08:25:33 +02:00
Nicola Soranzo 99b86c082c Merge branch 'release_22.01' into dev 2022-05-05 01:20:04 +01:00
John Chilton 9b8712f4bc Merge pull request #13860 from mvdbeek/move_tus_middleware_after_x_forwarded_host_middleware 
[22.01] Move TusMiddleware so XForwardedMiddleware runs first
 2022-05-04 19:24:15 -04:00
Nicola Soranzo 3988b54edc Replace deprecated Docker images for CircleCI 
See https://discuss.circleci.com/t/legacy-convenience-image-deprecation/41034
 2022-05-04 23:05:38 +01:00
Nicola Soranzo 02e36473a3 Split API tests in 2 jobs 2022-05-04 23:05:13 +01:00
Nicola Soranzo 1155b01784 Update GitHub action versions 2022-05-04 23:05:12 +01:00
Nicola Soranzo d93e49d970 Add `kind/enhancement` label to Python dep update PRs 2022-05-04 23:05:12 +01:00
Nicola Soranzo 3c805558e0 Add directories for auth label 2022-05-04 23:05:11 +01:00
John Chilton b84aec9ec3 Improved typing of Galaxy model store related stuff. 2022-05-04 12:11:17 -04:00
mvdbeek 4ca0d63c3b Merge branch 'release_22.01' into dev 2022-05-04 17:10:29 +02:00
Marius van den Beek 66b7e63c7d Merge pull request #13853 from mvdbeek/bump_datatsets_cli_version 
[22.01] Bump ncb-datasets-cli dependency to 13.14.0
 2022-05-04 17:08:54 +02:00
mvdbeek da1dd283f3 Add @TOOL_VERSION@ token for NCBI Datasets Genomes 2022-05-04 16:34:09 +02:00
John Chilton 329fb06c9e Fix workflow bookmarking API. 
And drop client-side hack that I assume was working around it. I tried dropping the tags argument that seems like shouldn't be needed and the results were not being persisted. Presumably someone realized the tags caused a flush and so sticking them in there worked around a bug related to a missing flush in this API.
 2022-05-04 10:12:25 -04:00
Michael R. Crusoe dd77026527 galaxy-tool-util: better link in the README 2022-05-04 15:25:42 +02:00